R. sphaeroides

Revision as of 01 August 2013 02:21 by admin (Comments | Contribs)

Rhodobacter sphaeroides strain 2.4.1. The R. sphaeroides 2.4.1 consists of a circular chromosome of 3,188,609 bp and five plasmids of 114,045 bp, 114,178 bp, 105,284 bp, 100,828 bp and 37,100 bp in length, respectively.


Read source

The paired-end illuminia read data of R. sphaeroides were downloaded from Gage-B

Sequence assembly

There are eight assemblers, ABySS, CABOG, MaSuRCA, MIRA, SGA, SOAPdenovo, SPAdes 2.5 and Velvet, used in the data, and the scaffolding results were downloaded from SPAdes website

Contig integrator

Contigs

Evaluation

  • Benchmark genome
R. sphaeroides 2.4.1
  • Evaluated by QUAST
QUAST (QUAST v2.1)
Running QUAST needs gene and sequence information.
Basic statisitcs ABySS CABOD MaSuRCA SGA SOAPdenovo SPAdes 2.5 Velvet CISA
# contigs 382 131 52 733 185 40 143 35
Largest contig 71578 177098 241348 44874 204500 739647 236829 740054
Total length 5380708 5420940 5433046 5321914 5344353 5379795 5356258 5469099
NG50 135613 431479 337861 25512 456635 485493 247748 487570
Misassemblies
# misassemblies 4 15 15 3 1 3 9 11
Misassembled contigs length　 155883 1987058 765654 24763 90965 94799 723259 2399227
Genome statistics
Genome fraction (%) 98.444 99.334 99.009 97.438 98.099 98.554 97523 99.38
# genes 5819 + 64 part　 5965 + 34 part　 5964 + 34 part　 5635 + 231 part　 5839 + 44 part　 5950 + 27 part　 5604 + 275 part　 5980 + 28 part　
# mismatches per 100 kbp 6.62 4.43 8.96 0.7 8.16 2.07 5.93 6.08'
# indels per 100 kbp 7.57 5.86 5.95 2 5.69 2.39 30.28 2.78
# N's per 100kbp 116.43 17.43 7.49 0 8.51 15.24 783.91 0.04